Department of Agronomy, Iowa State University, Ames, Iowa 50011.
Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, Iowa 50011.
Plant Physiol. 2020 Feb;182(2):977-991. doi: 10.1104/pp.19.00752. Epub 2019 Nov 18.
Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize () and sorghum (), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.
通过大规模全基因组关联研究（GWAS）确定植物根系结构（RSA）的遗传控制，需要高通量的根系表型分析流水线。我们开发了 Core Root Excavation using Compressed-air（CREAMD），这是一种用于田间生长的根系清洁的高通量流水线，以及 Core Root Feature Extraction（COFE），这是一种从图像中提取 RSA 特征的半自动流水线。CREAMD-COFE 应用于玉米（）和高粱（）的多样性面板，分别包含 369 和 294 个基因型。从超过 3300 个玉米根和超过 1470 个高粱根的图像中提取了 6 个 RSA 特征。基于单核苷酸多态性（SNP）的 GWAS 在玉米中鉴定出 87 个 TAS（性状相关 SNP），代表了 77 个基因和 115 个 TAS 在高粱中。通过表达读取深度 GWAS 还鉴定出了另外 62 个与玉米 RSA 相关的基因。在 139 个与玉米 RSA 相关的基因（或其同源物）中，有 22 个（16%）已知会影响玉米或其他物种的 RSA。此外，26 个与 RSA 相关的基因与先前显示会影响 RSA 的基因有共同调节作用，51 个（37%的 RSA 相关基因）本身就是另一个与 RSA 相关的基因的跨定量性状基因座。最后，发现玉米和高粱的 RSA 相关基因包括 7 对同源基因，这表明了形态跨分类群的调控具有保守性。
